Add more pre-commit checks

[Zethson]

Hey,

finally solves #1563

I added:

    -   id: trailing-whitespace
    -   id: end-of-file-fixer
    -   id: check-added-large-files
    -   id: check-case-conflict
    -   id: check-toml
    -   id: check-yaml
    -   id: check-merge-conflict
    -   id: detect-private-key

They are super super fast, so speed is not a concern.

Signed-off-by: zethson [email protected]

[codecov]

Codecov Report

Merging #1848 (547c422) into master (bcfa925) will increase coverage by 0.00%.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1848   +/-   ##
=======================================
  Coverage   71.21%   71.22%           
=======================================
  Files          92       92           
  Lines       11181    11181           
=======================================
+ Hits         7963     7964    +1     
+ Misses       3218     3217    -1     

Impacted Files	Coverage Δ
scanpy/preprocessing/_simple.py	80.14% <0.00%> (ø)
scanpy/plotting/_dotplot.py	87.16% <0.00%> (+0.37%)	⬆️

[ivirshup]

Only thing that needs to change is the added large file.

Could you try building the docs and checking if anything gets added? The scanpy.plotting.rst file has been weird in the past. I think it's at least started being consistent with newer versions of sphinx, but it'd be good to check.

I would like it if the yaml and toml checks would also do formatting, but up to you on including that.

[Zethson]

Could you try building the docs and checking if anything gets added? The scanpy.plotting.rst file has been weird in the past. I think it's at least started being consistent with newer versions of sphinx, but it'd be good to check.

The pbmc data in the docs folder does indeed get downloaded when building the docs.
Do you want me to include this path into the .gitignore?

[ivirshup]

Do you want me to include this path into the .gitignore?

👍

[Zethson]

Do you want me to include this path into the .gitignore?

+1

Done.

[ivirshup]

One last thing, could you exclude the test data files from any automatic formatting? I guess it's good to know that new lines at the end of files doesn't matter, but I'd prefer to keep those files exactly as they were written by spaceranger/ zarr.

[Zethson]

@ivirshup

exclude: scanpy/tests/_data

Added for trailing-whitespace and end-of-file-fixer.

[ivirshup]

Do revert the changes those made as well please!

[Zethson]

@ivirshup Done.

[ivirshup]

Great, thanks